Eli Wright raises his fist as he kisses his partner Don Wright, having just been married in Linn Park, at the Jefferson County Courthouse in Birmingham on Monday.
Photograph: Hal Yeager/AP

Same-sex couples in Alabama were flocking to the state’s courthouses, where some were able to apply for marriage licenses while others were turned away by probate judges refusing to follow a higher court’s ruling to overturn the state’s ban on gay marriage.

The US supreme court on Monday refused to stop same-sex marriages from beginning in Alabama, denying the state’s request to extend a hold on the ruling that overturned the state’s ban on gay marriages.

In a 7-2 ruling issued moments after the first couples began entering Alabama courthouses to apply for marriage licenses on Monday, the supreme court said it would not grant the state’s request for a stay, certifying that the federal government permits same-sex marriages in the state. Justices Clarence Thomas and Antonin Scalia were the only two to dissent.

Alabama governor Robert Bentley said in a statement that he agrees with Thomas’ and Scalia’s dissent – specifically their claim that the court has taken a “cavalier attitude towards the states”.

He said that the court’s decision has created confusion in the state, and that he will not take action against probate judges who ignore the order or follow it.

“Probate judges have a unique responsibility in our state, and I support them,” said Bentley. “I will not take any action against Probate Judges, which would only serve to further complicate this issue.”

Alabama attorney general Luther Strange said he had advised probate judges on Monday to speak to their attorneys and professional associations about how to respond to the supreme court’s ruling.

At least six counties were granting licenses to same-sex couples by mid-day Monday: Jefferson, Montgomery, Madison, Etowah, Coffee and Chilton.

At least nine counties refused licenses to same-sex couples, while five more refused licenses to anyone, straight or gay. Their refusal follows a Sunday night order from the state’s chief justice not to issue licenses for same-sex weddings.

Pike County probate judge Wes Allen that he would not issue the licenses so he could adhere to his Christian beliefs.

“The people of Pike County elected me to perform my duties and they also elected me because of who I am and the values I live by,” Allen told The Troy Messenger. “I am choosing to take the Pike County Probate Office out of the marriage licensing business altogether. That is completely within my rights under the laws of Alabama.”

Convington County probate judge Ben Bowden said he would not issue the licenses because he does not believe the federal judge’s decision requires him to do so. Marengo County probate judge Laurie Hall said her office would no longer perform marriages and that she would not sign licenses.

Celebrated by well-wishers, and a few protestors, Alabama couples on Monday married inside and outside courthouses in Birmingham, Huntsville and Montgomery. Some couples married in these cities instead of their home counties because their local judges refused to issue the licenses.

“This is a happy day for all of these couples, and if you can’t be happy for people, then I’m sorry,” King said. “If someone can’t understand the joy and happiness of others, then I don’t know what else I can say.”

The two couples whose lawsuit led to the ban being struck down – Cari Searcy and Kimberly McKeand and James Strawser and John Humphrey – were at Mobile Government Plaza waiting to file marriage and adoption documents.

Searcy and McKeand were there to file adoption papers that will allow Searcy to legally adopt McKeand’s biological child. Strawser and Humphrey are hoping to apply for their marriage license.

Equality Alabama and ACLU Alabama have created a hotline for people that encounter problems while applying for licenses on Monday.

Alabama supreme court chief justice Roy Moore has been advising judges not to follow a federal judge’s ruling that the state’s ban on same-sex marriage is unconstitutional. Sunday’s order, however, was his first official attempt to stop the weddings from happening.

His order defies the supremacy clause of the US constitution, which says federal law takes precedence over state law.

“Effective immediately, no probate judge of the State of Alabama nor any agent or employee of any Alabama probate judge shall issue or recognize a marriage license that is inconsistent” with state law, Moore said in the order, which was issued late on Sunday night.

He went on to say that if any judge did grant such licenses, it would be the responsibility of Alabama governor Robert Bentley “to ensure the execution of the law”.

Last month, a federal judge ruled the state’s ban on same-sex marriage to be unconstitutional. The decision was immediately put on hold pending appeal, but the stay expired on Monday morning.

“It’s not 100% clear that their hand can be forced until there is a definitive supreme court ruling,” Levy said. “Once there is a definitive supreme court ruling, then that becomes binding throughout the country.”

The US supreme court said last month it would pick up same-sex marriage cases from four states in the sixth circuit court of appeals, which ruled against lower court decisions striking down the bans, ending a streak of decisions by appellate courts in favor of marriage equality. A decision would clarify the patchwork of conflicting rulings in which some judges have upheld bans on same-sex marriage, which others struck them down.

If the supreme court rules that same-sex marriage bans are illegal, people who are being denied licenses by judges could go to a higher court and get an order forcing the judge to provide the documents. “And if they didn’t, presumably the judges could be removed,” said Levy.

Levy said the situation is parallel to what happened with the supreme court’s 1954 Brown v Board of Education ruling – which said it is illegal for there to separate schools for children based on their race. After that decision was made, people still had to get orders forcing schools to integrate.

One of the iconic images from the aftermath of that decision is tied to Alabama – when governor George Wallace blocked black students from entering the University of Alabama in 1963. The National Guard had to be sent to the campus to help it integrate.

Moore has long railed against same-sex couples and has twice advised probate judges that they are not required to issue licenses, because the move to allow them was ordered by a federal judge.

“Interference with the right of state courts to make independent judgments based on their own view of the US constitution is a violation of state sovereignty,” Moore wrote in his second letter, according to al.com.

Moore is known for making inflammatory statements – in 2003 he was removed from his position as the state’s chief justice when he refused to obey a government order to remove a 5,280lb granite Ten Commandments monument from the Alabama judicial building.